Unusual Chipseq Data

Question

[Jarus]

HI, I am looking at some ChIPSeq data that is rather unusual. The forward and reverse read form deep thin stacks. Their width is mostly just above the read length of 75 bp. The 'peaks' (pseudo-peaks?) are distributed well across the mouse genome. Have any of you see this? What could be the reason? This experiment is investigating transcription factor binding ....

Thanks! Jarus

Answer 1

[Sean Davis]

It sounds like you might have a problem with PCR duplicates. This might arise because of inadequate starting DNA, for example. A thorough QC evaluation and perhaps some forensic bioinformatics are probably warranted before proceeding with your analysis.